| name | chembl-molecule-search |
| description | Use this skill to search ChEMBL molecules by keyword and return a compact compound summary. Do not use it for local chemistry calculations or unsupported bulk export. |
Purpose
Search ChEMBL by free-text query and return compact compound summaries suitable for quick cheminformatics triage.
When to use
- You need a ChEMBL identifier and basic compound summary for a known drug or molecule name.
- You want a lightweight compound lookup before deeper cheminformatics or screening workflows.
When not to use
- You need local descriptor calculation or docking.
- You need bulk export of a large ChEMBL slice.
- You need offline execution.
Inputs
- Query string
- Optional result limit and output path
Outputs
- JSON payload with query metadata and compact molecule summaries
Requirements
- Python 3.10+
- Network access to
www.ebi.ac.uk
Procedure
- Run
python3 skills/drug-discovery-and-cheminformatics/chembl-molecule-search/scripts/search_chembl_molecules.py --query imatinib --limit 1 --out skills/drug-discovery-and-cheminformatics/chembl-molecule-search/assets/chembl_imatinib.json.
- Inspect
molecules for chembl_id, preferred_name, molecule_type, max_phase, canonical_smiles, and selected properties.
- Use the returned ChEMBL IDs in downstream compound-knowledge workflows when needed.
Validation
- Command exits successfully.
molecules contains at least one ChEMBL result for a known query.- The first result has a non-empty
chembl_id and molecule summary fields.
Failure modes and fixes
- No hits: refine the query or use a more canonical drug name.
- Too many hits: lower
--limit and inspect the top results manually.
- HTTP errors: retry later and keep the query simple for smoke verification.
Safety and limits
- Knowledge lookup only.
- This skill does not perform synthesis planning, structure optimization, or wet-lab decision making.
Example
python3 skills/drug-discovery-and-cheminformatics/chembl-molecule-search/scripts/search_chembl_molecules.py --query imatinib --limit 1
Provenance
Related skills
clinicaltrials-study-search
